Integrated mRNA and miRNA profiles expression of liver between Jinhua and Landrace pigs
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ABSTRACT:
PROVIDER: PRJNA512179 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8379830.fastq.gz | Fastqsanger.gz | |||
| SRR8379840.fastq.gz | Fastqsanger.gz | |||
| SRR8379831.fastq.gz | Fastqsanger.gz | |||
| SRR8379832.fastq.gz | Fastqsanger.gz | |||
| SRR8379833.fastq.gz | Fastqsanger.gz |
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Project description:Jinhua and Landrace pigs fecal samples Raw sequence reads
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Project description:To explore the molecular mechanisms of fat metabolism and deposition in pigs, an experiment was conducted to identify hepatic mRNAs and miRNAs expression and determine the potential interaction of them in two phenotypically extreme pig breeds.
2018-12-30 | GSE124484 | GEO
Project description:ObjectiveTo explore the molecular mechanisms of fat metabolism and deposition in pigs, an experiment was conducted to identify hepatic mRNAs and miRNAs expression and determine the potential interaction of them in two phenotypically extreme pig breeds.MethodsmRNA and miRNA profiling of liver from 70-day Jinhua (JH) and Landrace (LD) pigs were performed using RNA sequencing. Blood samples were taken to detect results of serum biochemistry. Bioinformatics analysis were applied to construct differentially expressed miRNA-mRNA network.ResultsSerum total triiodothyronine (TT3) and total thyroxine (TT4) were significantly lower in Jinhua pigs, but the content of serum total cholesterol (TCH) and low-density lipoprotein cholesterol (LDLC) were strikingly higher. A total of 467 differentially expressed genes (DEGs) and 35 differentially expressed miRNAs (DE miRNAs) were identified between JH and LD groups. Gene ontology analysis suggested that DEGs were involved in oxidation-reduction, lipid biosynthetic and lipid metabolism process. Interaction network of DEGs and DE miRNAs were constructed, according to target prediction results.ConclusionWe generated transcriptome and miRNAome profiles of liver from Jinhua and Landrace pig breeds which represent distinguishing phenotypes of growth and metabolism. The potential miRNA-mRNA interaction networks may provide a comprehensive understanding in the mechanism of lipid metabolism. These results serve as a basis for further investigation on biological functions of miRNAs in the porcine liver.
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Project description:Using Jinhua and Landrace pigs as fat and lean models, we present a comprehensive transcriptome-wide m6A profiling in adipose and muscle tissues from these two pig breeds.The results show m6A is widely spread and highly conserved in pig mRNA. m6A occurs in the conserved sequence motif of GGACU and exhibits a unique topology in pig. m6A peak enrichment correlates positively with gene expression, and transcripts with m6A at 5’UTR or CDS are correlated with gene activation than those at 3’UTR. Common m6A peaks in both layer of backfat from Landrace (L-LB) and Jinhua (J-LB) pigs are involved in lipid metabolism, while common m6A peaks in both longissimus dorsi muscle from Landrace (L-LDM) and Jinhua (J-LDM) mapped to muscle development, suggesting m6A-containing genes are involved in many biological processes especially related to tissue-specific functions.
2018-10-05 | GSE87625 | GEO
Project description:Backfat thickness is one of the most important traits of commercially raised pigs. Meishan pigs are renowned for having thicker backfat than Landrace pigs. To examine the genetic factors responsible for the differences, we first produced female crossbred pig lines by mating Landrace (L) × Large White (W) × Duroc (D) females (LWD) with Landrace (L) or Meishan (M) boars (i.e., LWD × L = LWDL for Landrace offspring and LWD × M = LWDM of the Meishan offspring). We confirmed that LWDM pigs indeed had a thicker backfat than LWDL pigs. Next, we performed gene expression microarray analysis (in both genetic lines) to examine differentially expressed genes (DEGs) in energy metabolism-related tissues, subcutaneous adipose (fat), liver, and longissimus dorsi muscle tissues. We analyzed the annotation of DEGs (2-fold cutoff) to functionally categorize them by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The number of DEGs in muscle tissues of both lines was much less than that in fat and liver tissues, indicating that DEGs was much lesser in muscle tissues (in both genetic lines) than in fat and liver tissues, thus indicating that DEGs in muscle tissues may not contribute much to differences in backfat thickness. In contrast, several genes related to muscle (in fat tissue) and fatty acid and glucose metabolism (in the liver) were more upregulated in LWDM pigs than LWDL pigs, indicating that those DEGs might be responsible for differences in backfat thickness. The different genome-wide, gene expression profiles in the fat, liver, and muscle tissues between breeds can provide useful information for pig breeders.
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Project description:The intestinal microbiome is critically important in shaping a variety of host physiological responses. However, it remains elusive on how gut microbiota impacts overall growth and more specifically, adipogenesis. Using the pig as an animal model, we compared the differences in bacterial community structure throughout the intestinal tract in two breeds (Landrace and Jinhua) of pigs with distinct phenotypes. The Landrace is a commercial purebred and the Jinhua is a Chinese indigenous, slow-growing breed with high propensity for fat deposition. Using 16S rRNA gene sequencing, we revealed that the bacterial communities are more diverse in the duodenum, jejunum, and cecum of Jinhua pigs than in those of Landrace pigs, whereas the ileal and colonic microbiota show a similar complexity between the two breeds. Furthermore, a number of bacterial taxa differentially exist in Jinhua and Landrace pigs throughout the entire intestinal tract, with the jejunal and ileal microbiome showing the greatest contrast. Functional prediction of the bacterial community suggested increased fatty acid biosynthesis in Jinghua pigs, which could partially explain their adiposity phenotype. Further studies are warranted to experimentally verify the relative contribution of each enriched bacterial species and their effect on adipogenesis and animal growth.
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Project description:Hezuo pigs are known in China for early sexual maturity. In this study, we obtained transcriptome data from testicular tissues of 30-day-old and 120-day-old Hezuo and Landrace pigs. Through comparative analysis of their differences, we searched for some genes related to the regulation of precocious sexual traits in male cooperating pigs and revealed their molecular regulatory mechanisms, which can then provide references for the diagnosis and treatment of precocious sexual diseases in humans and for accelerating the breeding of high-fertility animals.
2021-08-31 | GSE171756 | GEO
Project description:Hezuo pigs are known in China for early sexual maturity. In this study, we obtained small RNA-Seq data from testicular tissues of 30-day-old and 120-day-old Hezuo and Landrace pigs. Through comparative analysis of their differences, we searched for some miRNAs related to the regulation of precocious sexual traits in male cooperating pigs and revealed their molecular regulatory mechanisms, which can then provide references for the diagnosis and treatment of precocious sexual diseases in humans and for accelerating the breeding of high-fertility animals.
2022-11-18 | GSE192462 | GEO
Project description:The aim of this study was to identify differentially expressed genes and pathways in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. We confirmed the expression patterns for a subset of genes by qRT-PCR. Pathway analysis revealed functionally related genes, and indicated commonalities and differences between the breed types and developmental ages evaluated. Results from qRT-PCR analysis confirmed the expression patterns observed on the array for most of the genes tested (85%). This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types.
2010-04-22 | GSE21412 | GEO
Project description:The aim of this study was to identify differentially expressed genes and pathways in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. We confirmed the expression patterns for a subset of genes by qRT-PCR. Pathway analysis revealed functionally related genes, and indicated commonalities and differences between the breed types and developmental ages evaluated. Results from qRT-PCR analysis confirmed the expression patterns observed on the array for most of the genes tested (85%). This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types. This study utilized the Swine Protein-Annotated Oligonucleotide Microarray which contains 20,400 70-mer oligonucleotides (http://www.pigoligoarray.org). Total RNA was isolated from fetuses obtained from gilts at each gestational age (n=3 crossbred gilts; n=4 Piau gilts) and RNA from 3 fetuses per litter was pooled. Samples were evaluated with a connected loop design using 13 slides such that six breed comparisons and seven age comparisons were performed. Fluorescence intensity data was LOESS normalized and analyzed with a mixed model.
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